rs10915985

Variant names:

• chr1-226352049-C-T
• rs10915985
• ENST00000690647.2:n.460-1492C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000690647.2(ENSG00000289348):​n.460-1492C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,020 control chromosomes in the GnomAD database, including 9,506 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (9506 hom., cov: 31)
• Consequence: ENSG00000289348 ENST00000690647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 9 publications found

Genes affected

ENSG00000289348 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289348	ENST00000690647.2	n.460-1492C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50572 AN: 151902 Hom.: 9509 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.346

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.333 AC: 50567 AN: 152020 Hom.: 9506 Cov.: 31 AF XY: 0.328 AC XY: 24335 AN XY: 74294

African (AFR) AF: 0.182 AC: 7532 AN: 41452

American (AMR) AF: 0.359 AC: 5493 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1904 AN: 3470

East Asian (EAS) AF: 0.114 AC: 588 AN: 5170

South Asian (SAS) AF: 0.332 AC: 1597 AN: 4806

European-Finnish (FIN) AF: 0.321 AC: 3395 AN: 10562

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28881 AN: 67954

Other (OTH) AF: 0.342 AC: 724 AN: 2114

Alfa AF: 0.369 Hom.: 12007

Bravo AF: 0.327

Asia WGS AF: 0.220 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		-0.16

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10915985; hg19: chr1-226539750;